Computational protocol: Barriopsis iraniana and Phaeobotryon cupressi: two new species of the Botryosphaeriaceae from trees in Iran

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Protocol publication

[…] The nucleotide sequences were aligned with ClustalX v1.83 (), using the following parameters: pairwise alignment parameters (gap opening = 10, gap extension = 0.1) and multiple alignment parameters (gap opening = 10, gap extension = 0.2, transition weight = 0.5, delay divergent sequences = 25 %). Alignments were checked and manual adjustments were made where necessary. Phylogenetic analyses were carried out using PAUP v4.0b10 () for maximum-parsimony (MP) analysis and MrBayes v 3.0b4 () for the Bayesian analysis. Trees were visualised with TreeView (). Maximum-parsimony analysis was performed using the heuristic search option with 1 000 random taxon additions and tree bisection and reconnection (TBR) as the branch-swapping algorithm. All characters were unordered and of equal weight and gaps were treated as fifth character. Branches of zero length were collapsed and all multiple, equally parsimonious trees were saved. The robustness of the most parsimonious trees was evaluated by 1 000 bootstrap replications (). Other measures used were consistency index (CI), retention index (RI) and homoplasy index (HI). A partition homogeneity test was done to determine the possibility of combining the ITS and EF1-α datasets (, ).Bayesian analyses employing a Markov Chain Monte Carlo (MCMC) method were performed. The general time-reversible model of evolution (), including estimation of invariable sites and assuming a discrete gamma distribution with six rate categories (GTR+I+Γ) was used. Four MCMC chains were run simultaneously, starting from random trees, for 106 generations. Trees were sampled every 100th generation for a total of 104 trees. The first 103 trees were discarded as the burn-in phase of each analysis. Posterior probabilities () were determined from a majority-rule consensus tree generated from the remaining 9 000 trees. The analysis was repeated three times starting from different random trees to ensure trees from the same tree space were being sampled during each analysis. […]

Pipeline specifications

Software tools Clustal W, PAUP*, MrBayes, TreeViewX
Application Phylogenetics
Organisms Cupressus sempervirens